Running it low on fuel creates a lot more heat in injection pump and the electronics on top of it. Sounds like VP-44 related issue more than the ecm, because it started right after you ran it low on fuel. Get them to verify the exact problem, and NOT just change out both, or the wrong one , or find another qualified shop. Check lift pump pressure to verify it is good also. ECM failures don't seem to happen very often. Have you tried the APPS reset after battery disconnect, did it help/change anything at all?

 

Just got off the phone with Cleo. She said you need a new VP44.

 

Who's Cleo, the diagnostic queen.